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       mgd77manage - Manage extra columns in MGD77+ files


       mgd77manage    NGDC-ids   [   -A[+]a|c|d|D|e|E|g|i|n|t|Tfileinfo   ]   [   -Cf|g|e   ]   [
       -Dabbrev1,abbrev2,... ] [ -Eempty ] [ -F ] [ -Iabbrev/name/unit/t/scale/offset/comment ] [
       -Ne|k|m|n ] [ -Q[b|c|l|n][[/]threshold] ] [ -V ] [ -bi[s|S|d|D[ncol]|c[var1/...]] ]


       mgd77manage  deals  with maintaining extra custom columns in MGD77+ netCDF files.  You can
       either delete one or more columns, add a new column, update an existing  column  with  new
       data,  or  supply  error  correction  information (*.e77 files).  New data may come from a
       table (ASCII unless -b is used), be based on  existing  columns  and  certain  theoretical
       expressions,  or  they  may  be  obtained by sampling a grid (choose between GMT grid or a
       Sandwell/Smith Mercator *.img grid) along track.  The new data will  be  appended  to  the
       MGD77+  file in the form of an extra data column of specified type.  The data file will be
       modified; no new file will be created.  For the big issues,  see  the  DISCUSSION  section

              Can be one or more of five kinds of specifiers:
              1) 8-character NGDC IDs, e.g., 01010083, JA010010etc., etc.
              2) 2-character <agency> codes which will return all cruises from each agency.
              3)  4-character  <agency><vessel>  codes,  which will return all cruises from those
              4) =<list>, where <list> is a table with NGDC IDs, one per line.
              5) If nothing is specified we return all cruises in the data base.
              (See mgd77info -L for agency and vessel codes).  The ".mgd77" or  ".nc"  extensions
              will  automatically  be  appended, if needed (use -I to ignore certain file types).
              Cruise files will be looked for first in the current directory and  second  in  all
              directories  listed  in  $MGD77_HOME/mgd77_paths.txt  [If $MGD77_HOME is not set it
              will default to $GMT_SHAREDIR/mgd77].


       No space between the option flag and the associated arguments

       -A     Add a new data column.  If an existing column with the  same  abbreviation  already
              exists  in  the  file  we  will  cowardly refuse to update the file. Specifying -A+
              overcomes this reluctance (However, sometimes an existing column cannot be upgraded
              without  first deleting it; if so you will be warned).  Select a column source code
              among a, c, d, D, e, g, i, n, t,  or  T;  detailed  descriptions  for  each  choice

              a  Append filename of a single column table to add.  File must have the same number
              of rows as the MGD77+ file. If no file is given we read from stdin instead.

              c Create a new column that derives from existing data or formulas  for  corrections
              and  reference  fields.   Append  c  for  the  Carter  corrections  subtracted from
              uncorrected depths, g for the IGF gravity reference field (a.k.a "normal gravity"),
              m  for the IGRF total field magnetic reference field, and r for recomputed magnetic
              anomaly (append 1 or 2 to specify which  total  field  column  to  use  [1]).   For
              gravity  we  choose  the reference field based on the parameter Gravity Theoretical
              Formula Code in the cruise's MGD77 header.  If this is not set  or  is  invalid  we
              default  to the IGF 1980.  You can override this behaviour by appending the desired
              code: 1 = Heiskanen 1924, 2 = International 1930, 3 = IGF1967, or 4 = IGF1980.

              d  Append filename of a two-column table with the first  column  holding  distances
              along track and the second column holding data values.  If no file is given we read
              from stdin instead.  Records with matching distances in the  MGD77+  file  will  be
              assigned  the  new  values;  at other distances we set them to NaN.  Alternatively,
              give upper case D instead  and  we  will  interpolate  the  column  at  all  record
              distances.   See  -N  for choosing distance units and -C for choosing how distances
              are calculated.

              e Expects to find an e77 error/correction  log  from  mgd77sniffer  with  the  name
              NGDC_ID.e77 in the current directory or in $MGD77_HOME/E77; this file will examined
              and used  to  make  modifications  to  the  header  values,  specify  a  systematic
              correction  for  certain columns (such as scale and offset), specify that a certain
              anomaly should be recalculated from the observations (e.g.,  recalculate  mag  from
              mtf1 and the latest IGRF), and add or update the special column flag which may hold
              bitflags (0 = GOOD, 1 = BAD) for each data field in the standard  MGD77  data  set.
              Any  fixed  correction  terms  found (such as needing to scale a field by 0.1 or 10
              because the source agency used incorrect units) will be written  as  attributes  to
              the  netCDF MGD77+ file and applied when the data are read by mgd77list.  Ephemeral
              corrections such as those determined by crossover analysis are not kept in the data
              files but reside in correction tables (see mgd77list for details).  By default, the
              first character of each header line in the e77 file (which is ?, Y or  N)  will  be
              consulted  to  see  if  the  corresponding  adjustment  should  be applied.  If any
              undecided settings are found (i.i, ?) we will abort  and  make  no  changes.   Only
              records  marked  Y  will be processed.  You can override this behavior by appending
              one or more modifiers to the -Ae command: h will ignore all header  corrections,  f
              will  ignore  all  fixed  systematic  trend  corrections,  n,  v, and s will ignore
              bitflags pertaining to navigation, data values, and data slopes, respectively.  Use
              -A+e  to  replace  any  existing  E77  corrections in the file with the new values.
              Finally, e77 corrections will not be applied if the E77 file has not been verified.
              Use -AE to ignore the verification status.

              g  Sample a GMT geographic (lon, lat) grid along the track given by the MGD77+ file
              using bicubic interpolation (however, see -Q).  Append name of a GMT grid file.

              i Sample a Sandwell/Smith Mercator *.img grid along the track given by  the  MGD77+
              file  using bicubic interpolation (however, see -Q).  Append the img grid filename,
              followed by the comma-separated data scale (typically 1 or 0.1), the IMG file  mode
              (0-3),  and optionally the img grid max latitude [80.738].  The modes stand for the
              following: (0) Img files with no constraint code, returns data at all  points,  (1)
              Img  file  with  constraints  coded,  return  data at all points, (2) Img file with
              constraints coded, return data only at constrained points and  NaN  elsewhere,  and
              (3) Img file with constraints coded, return 1 at constraints and 0 elsewhere.

              n  Append  filename  of a two-column table with the first column holding the record
              number (0 to nrows - 1) and the second column holding data values.  If no  file  is
              given  we  read  from  stdin  instead.  Records with matching record numbers in the
              MGD77+ file will be assigned the new values; at other records we set them to NaN.

              t Append filename of a two-column table with  the  first  column  holding  absolute
              times  along  track and the second column holding data values.  If no file is given
              we read from stdin instead.  Records with matching times in the MGD77+ file will be
              assigned  the  new  values; at other times we set them to NaN.  Alternatively, give
              upper case T instead and we will interpolate the column at all record times.

       -C     Append  a  one-letter  code  to  select  the  procedure  for  along-track  distance
              calculation when using -Ad|D (see -N for selecting distance units):
                   f Flat Earth distances.
                   g Great circle distances [Default].
                   e Geodesic distances on current GMT ellipsoid.

       -D     Give  a  comma-separated  list of column abbreviations that you want to delete from
              the MGD77+ files.  Do NOT use this option to remove columns that you are  replacing
              with  new  data  (use -A+ instead).  Because we cannot remove variables from netCDF
              files we must create a new file without the columns to be deleted.  Once  the  file
              is successfully created we temporarily rename the old file, change the new filename
              to the old filename, and finally remove the old, renamed file.

       -E     Give a single character that will be repeated to fill empty  string  values,  e.g.,
              '9' will yield a string like "99999..." [9].

       -F     Force  mode.   When this mode is active you are empowered to delete or replace even
              the standard MGD77 set of columns.  You better know what you are doing!

       -I     In addition to file information we must specify additional  information  about  the
              extra  column.  Specify a short (16 char or less, using lower case letters, digits,
              or underscores only) abbreviation for the selected data, its more descriptive name,
              the  data unit, the data type 1-character code (byte, short, float, int, double, or
              text) you want used for storage in the netCDF file, any scale and offset we  should
              apply  to  the data to make them fit inside the range implied by the chosen storage
              type, and a general comment (< 128 characters) regarding what these data represent.
              Note:  If  text  data type is selected then the terms "values" in the -A discussion
              refer to your text data.  Furthermore, the discussion  on  interpolation  does  not
              apply  and  the  NaN  value  becomes a "no string" value (see -E for what this is).
              Place quotes around terms with more than one word (e.g., "Corrected Depth").

       -N     Specify the distance unit used when using -Ad|D by appending e (meter), k  (km),  m
              (miles), or n (nautical miles). [Default is -Nk (km)].

       -Q     Quick   mode,   use   bilinear   rather   than   bicubic  interpolation  [Default].
              Alternatively, select the interpolation mode by adding b for B-spline smoothing,  c
              for  bicubic  interpolation, l for bilinear interpolation or n for nearest-neighbor
              value.  Optionally, append threshold in the range [0,1].  This  parameter  controls
              how close to nodes with NaN values the interpolation will go.  E.g., a threshold of
              0.5 will interpolate about half way from a non-NaN to a NaN node, whereas 0.1  will
              go  about  90%  of  the  way, etc. [Default is 1, which means none of the (4 or 16)
              nearby nodes may be NaN].  -Q0 will just return  the  value  of  the  nearest  node
              instead of interpolating.  This is the same as using -Qn.  Only relevant when -Ag|i
              is selected.

       -V     Selects verbose mode, which will send progress  reports  to  stderr  [Default  runs

       -bi    Selects  binary  input.   Append  s  for  single precision [Default is d (double)].
              Uppercase S or D will force byte-swapping.  Optionally, append ncol, the number  of
              columns  in your binary input file if it exceeds the columns needed by the program.
              Or append c if the input  file  is  netCDF.  Optionally,  append  var1/var2/...  to
              specify  the  variables  to be read.  This applies to the input 1- or 2-column data
              files specified under some of the -A options.  The  binary  input  option  is  only
              available for numerical data columns.


       To  append  Geosat/ERS-1  gravity  version  11.2  as  an  extra data column in the cruises and, storing the values as mGal*10 in a 2-byte short integer, try

       mgd77manage   01010047   01010008   -Ai   10/1/grav.11.2.img   -I    satgrav/"Geosat/ERS-1
       gravity"/"mGal"/s/10/0/"Sandwell/Smith version 11.2" -V

       To  append  a  filtered version of magnetics as an extra data column of type float for the
       cruise, and interpolate the filtered data at the times  given  in  the  MGD77+
       file, try

       mgd77manage   01010047   -AT   -I   filtmag/"Intermediate-wavelength   magnetic
       residuals"/"nTesla"/f/1/0/"Useful for looking for isochrons" -V

       To delete the existing extra columns satfaa, coastdist, and satvgg from all MGD77+  files,

       mgd77manage `cat allmgd77.lis` -D satfaa,coastdist,satvgg -V

       To create a 4-byte float column with the correct IGRF reference field in all MGD77+ files,

       mgd77manage `cat allmgd77.lis` -Acm -I  igrf/"IGRF  reference  field"/"nTesla"/f/1/0/"IGRF
       version 10 for 1990-2010" -V


       1. Preamble
       The  mgd77  supplement  is  an  attempt to (1) improve on the limited functionality of the
       existing mgg supplement, (2) incorporate some of the ideas from Scripps'  gmt+  supplement
       by  allowing  extra  data  columns,  and  (3)  add  new  capabilities  for managing marine
       geophysical trackline data stored  in  an  architecture-independent  CF-1.0-  and  COARDS-
       compliant netCDF file format.  Here are some of the underlying ideas and steps you need to
       take to maintain your files.

       2. Introduction
       Our starting point is the MGD77 ASCII data files distributed from NGDC  on  CD-ROMS,  DVD-
       ROMS,  and  via  FTP.   Using  Geodas  to  install the files locally we choose the "Carter
       corrected depth" option which will fill in the depth column using the two-way  traveltimes
       and  the Carter tables if twt is present.  This step yields ~5000 individual cruise files.
       Place these in one or more sub-directories of your choice, list these sub-directories (one
       per  line) in the file mgd77_paths.txt, and place that file in the directory pointed to by
       $MGD77_HOME; if not set this variable defaults to $GMT_SHAREDIR/mgd77.

       3. Conversion
       Convert the ASCII MGD77  files  to  the  new  netCDF  MGD77+  format  using  mgd77convert.
       Typically,  you  will  make  a  list  of  all the cruises to be converted (with or without
       extension), and you then run

            mgd77convert -Fa -Tc -V -Lwe+ `cat cruises.lis` > log.txt

       The verbose settings will ensure  that  all  problems  found  during  conversion  will  be
       reported.   The  new *.nc files may also be placed in one or more separate sub-directories
       and these should also be listed in the mgd77_paths.txt file.  We  suggest  you  place  the
       directories  with  *.nc  files  ahead  of the *.mgd77 directories.  When you later want to
       limit a search to files of a certain extension you should use the -I option.

       4. Adding new columns
       mgd77manage will allow you to add additional data columns to your *.nc files.   These  can
       be  anything,  including  text strings, but most likely are numerical values sampled along
       the track from a  supplied  grid  or  an  existing  column  that  have  been  filtered  or
       manipulated  for  a  particular purpose.  The format supports up to 32 such extra columns.
       See this man page for how to add columns.  You may later decide to remove  some  of  these
       columns  or  update the data associated with a certain column.  Data extraction tools such
       as mgd77list can be used to extract a mix of standard MGD77 columns (navigation, time, and
       the usual geophysical observations) and your custom columns.

       5. Error sources
       Before we discuss how to correct errors we will first list the different classes of errors
       associated with MGD77 data: (1) Header record errors occur when some  of  the  information
       fields in the header do not comply with the MGD77 specification or required information is
       missing.  mgd77convert will list  these  errors  when  the  extended  verbose  setting  is
       selected.   These  errors  typically  do not affect the data and are instead errors in the
       meta-data (2) Fixed systematic errors occur when a particular  data  column,  despite  the
       MGD77  specification,  has  been encoded incorrectly.  This usually means the data will be
       off by a constant factor such as 10 or 0.1, or in some cases even  1.8288  which  converts
       fathoms  to meters.  (3) Unknown systematic errors occur when the instrument that recorded
       the data or the processing that followed introduced signals that appear to  be  systematic
       functions  of time along track, latitude, heading, or some other combination of terms that
       have a physical or logical explanation.  These terms may sometimes  be  resolved  by  data
       analysis  techniques  such as along-track and across-track investigations, and will result
       in correction terms that when applied to the data will remove these unwanted signals in an
       optimal  way.   Because  these correction terms may change when new data are considered in
       their determination, such corrections are considered to be ephemeral. (4) Individual  data
       points  or sequences of data may violate rules such as being outside of possible ranges or
       in other ways violate sanity.  Furthermore, sequences of points that may be  within  valid
       ranges  may  give rise to data gradients that are unreasonable.  The status of every point
       can therefore be determined and this gives rise to bitflags GOOD or BAD.   Our  policy  is
       that error sources 1, 2, and 4 will be corrected by supplying the information as meta-data
       in the relevant *.nc files, whereas the corrections for error source 3 (because they  will
       constantly be improved) will be maintained in a separate list of corrections.

       6. Finding errors
       The  mgd77sniffer  is a tool that does a thorough along-track sanity check of the original
       MGD77 ASCII files and produces a corresponding *.e77 error log.  All  problems  found  are
       encoded in the error log, and recommended fixed correction terms are given, if needed.  An
       analyst may verify that the suggested corrections  are  indeed  valid  (we  only  want  to
       correct truly obvious unit errors), edit these error logs and modify such correction terms
       and activate them by changing the relevant code key (see mgd77sniffer for  more  details).
       mgd77manage  can  ingest  these  error  logs  and (1) correct bad header records given the
       suggestions in the log, (2) insert scale/offset correction terms to be used  when  reading
       certain  columns,  and  (3) insert any bit-flags found.  Rerun this step if you later find
       other problems as all E77 settings or flags will be recreated based on the latest E77 log.

       7. Error corrections
       The extraction program mgd77list allows for corrections to be applied on-the-fly when data
       are  requested.   First,  data  with BAD bitflags are suppressed.  Second, data with fixed
       systematic correction  terms  are  corrected  accordingly.   Third,  data  with  ephemeral
       correction  terms will have those corrections applied (if a correction table is supplied).
       All of these steps require the presence of the relevant meta-data and all can be overruled
       by  the  user.  In addition, users may add their own bitflags as separate data columns and
       use mgd77list's logical tests to further dictate which data are suppressed from output.


       The IGRF calculations are based on a Fortran program written by Susan  Macmillan,  British
       Geological  Survey,  translated  to C via f2c by Joaquim Luis, and adapted to GMT style by
       Paul Wessel.


       mgd77convert(1), mgd77list(1), mgd77info(1), mgd77sniffer(1) mgd77track(1) x2sys_init(1)


       Wessel, P., and W. H. F. Smith, 2013, The  Generic  Mapping  Tools  (GMT)  version  4.5.11
       Technical Reference & Cookbook, SOEST/NOAA.
       Wessel,  P.,  and  W.  H.  F.  Smith, 1998, New, Improved Version of Generic Mapping Tools
       Released, EOS Trans., AGU, 79 (47), p. 579.
       Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Mapping  Tools  Released,
       EOS Trans., AGU, 76 (33), p. 329.
       Wessel,  P.,  and W. H. F. Smith, 1995, New Version of the Generic Mapping Tools Released,, Copyright 1995 by the American Geophysical Union.
       Wessel, P., and W. H. F. Smith, 1991, Free  Software  Helps  Map  and  Display  Data,  EOS
       Trans., AGU, 72 (41), p. 441.
       The     Marine     Geophysical     Data     Exchange     Format     -     "MGD77",     see
       IGRF, see